Brennan's Secret
by NicHale
Summary: Brennan has kept a secret since she left for Maluku. She was pregnant with Booth's babies. When Cam needs help in solving the murder of a little boy Brennan has to hide her kids because she wants Booth to be happy. Will Booth ever find put about his other two kids? Rated T for language mostly.
1. Chapter 1

Brennan sat in her living room, thinking of the conversation she and Booth had outside of the Hoover building, and the time they spent together after it. Booth had apologized and said that it could never happen again and that he needed to move on. Tomorrow she would be leaving for Maluku with Daisy and Booth would be going to Maluku.

She was tempted to stay, but found out that everyone else was leaving too. Cam was the only one staying. She realized that they were all leaving because she was running from her feelings and afraid to admit them. She wanted to go to Booth that night and profess her undying love for him, but was afraid of what would happen if it didn't work out. Brennan couldn't bear to lose him and Booth didn't seem to understand that. He wanted to take the chance that might hurt them in the end and she couldn't do anything to hurt him or see him in pain, but that's what she did right?

She took his heart and broke it into a million little pieces. That was the only way to protect him from her. She felt bad for it but it was all she could do.

The pain he would experience now would be easier to get over compared to the pain caused by them getting together and then breaking up. She would never be able to get through it. She knew that if she had even a little piece of him she would only want more and if that was torn away from her, she would die. She loved him enough to let him move on with his life and find someone who could be there for him in ways she couldn't. She lay in bed, staring at the ceiling, thinking over her new revelation.

She walked into the kitchen and grabbed a bottle of water from the fridge. She was walking to the couch when she heard a knock on her front door. She walked over and opened it, surprised to see her partner standing there. She stepped back without saying a word and let him into her home. As she turned around she was pushed back into the front door. He kissed her hard and hitched her leg around his waist.

She was surprised when he kissed her, but responded quickly. She poured everything she had into that kissed and hoped he knew how she felt. He carried her back to her bedroom and made love to her, neither saying a word all night.

He kissed her forehead and they fell asleep in each other's arms. The next morning, she was disappointed to find that he left before she woke up and wondered if she had just imagined it all, but her body told her otherwise. She got up and got ready to head to the airport, constantly thinking about whether or not he would be there to say goodbye.

She called a cab service and picked up her bags before heading to the airport. She was met by all her friend at the airport, who had all come to say their goodbyes. She was slightly upset that Booth wasn't there, but she quickly got over it as she looked into the tear-stained face of her best friend. She pulled her into a hug and held the artist tightly.

"I'm going to miss you most Ange. You are the best friend I could ever ask for. I love you." This just made Angela cry harder and hold onto Brennan tighter. She turned to Jack and hugged him to.

"You know I love you too, right Jack?" He simply nodded and winked at her. "I will come and visit you guys in Paris every chance I get, ok?" They hugged her again and she turned to Cam.

"It was a pleasure working with you Dr. Brennan." Brennan hugged the pathologist and said, "You too, Dr. Saroyan." She pulled away and heard her flight being called for boarding. As she turned to leave she saw Booth standing there in his uniform and heard Angela say something about how hot men in uniforms were. She walked over to him and he pulled her into a quick hug.

"Listen, I know you have to go, but I just wanted to say I'm going to miss you and I'm sorry for last night. I shouldn't have forced myself on you like that. It was a mistake and it will never happen again. Now I have to go before they find out I went AWOL but, a year from today, meet me at the coffee cart on the mall." Brennan smiled nodded and turned away as the tears started running down her face. She grabbed her bags and headed for her flight.

As she got herself situated she couldn't help think about what Booth had said. Their being together was a mistake, and when he said that she just about lost it. This was exactly why she had said no to him in the first place. She knew that because of last night she would spend the rest of her life wanting him and quite possibly never being able to have him.

She knew that when she got back she would have to tell him exactly how she felt and could only hope that in a year he would still feel the same way about her. She laid her seat back and got ready for the day long ride to Maluku and mentally braced herself for a year with Daisy Wick.

After three weeks in Maluku, Brennan was beginning to miss Angela and decided she would surprise her for Christmas. Brennan had been sick for the past few days but brushed it off as a stomach bug. She made preparations for her trip to Paris including a video conference to her favorite entomologist. Brennan sat in her tent waiting for Jack to answer the call.

"Dr. B! How is Maluku?" Brennan smiled at her friend.

"Hey Jack. Maluku is ok. I wanted to ask you something. I want to surprise Angie for Christmas by coming there and I wanted to make sure you guys had room." Hodgins had a look on his face that said 'why didn't I think of that'.

"Sure, Brennan, Angela already set up your room. She wanted you to have your own room here." Brennan smiled and they talked for a while before she had to go. She was leaving in a few days and had to tie up a few loose ends before her temporary leave. A few days later she was still sick and decided that when she got to Paris she would see a doctor

. She sat in her seat on the plane going over her symptoms from the past week. She was constantly throwing up, she was moody, and her body was a lot more sensitive. She then remembered that she had been planning on going to Maluku and wasn't planning on having sex she had stopped taking her birth control a few weeks before leaving and when she and Booth had sex, he didn't wear a condom and she was too caught up the moment to even think about that.

Brennan was happy that she was going to be a mother, but was worried what would happen if she told Booth. She decided that she would wait until he got back to D.C. to evaluate her situation with him and then tell him.

She also decided that this would be her second present to Angela. She wouldn't be able to see her friend when she got there because she had her doctor's appointment and as Christmas present she would appear on Christmas morning, which was tomorrow. After seeing the doctor, who confirmed her thoughts, though she was shocked when he told her she was having twins, she went on a hunt for the perfect gift for Jack.

She sat in a café searching the internet for the perfect gift for the entomologist. She found online beautiful pictures of butterflies that were both aesthetically appealing and interesting to a person who loved bugs.

She also found a framed collection of insects that she knew Jack would love. She ordered them for overnight delivery and enjoyed the rest of the day. She waited until it was midnight before she went to Angela and Hodgins' apartment. She found the spare key, where Jack had put it, and let herself inside. She walked back to her room at the end of the hall and put her things down.

She wrapped her presents which were at the doorstep when she came to the house, before going to the living room and putting them under the tree with a card for Angela.

She had put her ultrasound pictures in it. The next morning she waited until she heard Jack and Angela get up before walking out into the living room. Angela's back was turned to her so she snuck up behind her, signaling Jack to stay quiet, and wrapped her arms around the artist's shoulders. Angela screamed and whirled around to face Brennan. She squealed gleefully and hugged her friend tightly.

"Ohmygod," she said so fast her words ran together. "When did you get here?" Brennan laughed at the excited but still slightly in shock expression on Angela's face.

"Yesterday morning. I am one of your Christmas gifts, so I figured that I would wait until this morning to see you. Hey, I have an idea, how about we open presents huh?" Angela was like a kid. She ran over to the tree and pulled out everyone's gifts and handed them out.

"I'm sorry I didn't get you much Ange, but I hope you like it," Brennan said as she handed over the card. Angela took it eagerly and tore it open. Angela had a confused look but then realization spread over her features and her lips pulled into a huge grin.

"Really?" Brennan smiled and nodded at her best friend, who squealed and tackled her. Jack looked at his gift and looked just as excited about his it as Angela was about hers. Jack and Angela decided to let Brennan stayed in Paris with them so that they could help her.

She would only be staying until she began showing, then she would be heading back to D.C. Jack and Angela decided that they would go back with her and would help her with the kids. She called the other doctor, who was co-heading the dig with her,

"Dr. Lyndon, this is Dr. Brennan. I am calling to inform you that I will be unable to return to the dig. Something personal has come up and I must return to the States. Please have Ms. Wick to pack up my things and send the artifacts to my Lab and my personal effects sent to this address," she gave the address to the Paris penthouse.


	2. Chapter 2

Well... I'm back finally. Sorry it took me so long. This second chapter will be shorter than the first but I will make up for it by making the third chapter twice as long as the other two. Hope y'all enjoy.

Disclaimer: because I forgot in the first chapter, I don't own Bones. Hart Hanson and fox do.

* * *

Brennan called Wendell and asked him to put all her things in storage when it arrived. "Angela, want to go baby shopping with me?" she asked one day. They would be leaving soon and she was just entering her second trimester. She knew Angela loved Paris and she loved it too. They walked into a baby boutique and picked out two dozen matching outfits for the babies.

Brennan was happy that she had great friends like Jack and Angela. She and Angela packed everything they needed away and sent it back to the states. They would leave the furniture because it would be their vacation house when they wanted to get away. They had a flight scheduled for the following morning, so they went to sleep and prepared for the next six months.

"I'm gonna miss it here," Angela said as they waited for Jack to return with coffee.

"Me too. I enjoyed my few months here. I'm sorry that you guys have to leave it all because of me." Angela patted her friend on the shoulder,

"We would do anything for you Bren." Brennan smiled and Jack sat down, handing out coffee. They boarded the plane and Brennan basically slept the whole way.

"Bren, we're here. Wake up." Brennan had already been awake when she heard the landing announcement but kept her eyes closed. She stood and they walked out to their cab. When she got into the cab she called the head of the Jeffersonian.

"Good morning Dr. Goodman. Today, Angela, Dr. Hodgins and I returned from overseas and I was curious if we could reopen the lab. Yes, I will be returning to work but I don't want anyone to know that I am back. Personal reasons that I am unable to say right now. Yes, we will be by later today to set up our offices. I will not be working with the FBI again until Booth gets back so, most of my work will be identifying bodies in Limbo. Yes. Thank you. You too. Bye."

They drove home and put their things away before heading to the Lab.

"Dr. B. Goodman said you were coming back and needed my help," Wendell said as he came over and hugged his mentor. The Lab was completely empty. She and Wendell talked as he helped her set up her office. She worked on setting up the light things and he moved the heavy stuff.

"So, what brings you guys back stateside?" Brennan figured that she could trust Wendell to keep her secret and she really felt like she was going to burst if she didn't tell someone.

"I'm pregnant, Jack and Ange came back to help me" She smiled and continued to work. "Wow, Dr. B congrats. Just so you know I'm here for you too. Just ask and I'll be there to help." He smiled. Brennan was shocked at the fact the she had such great friends. She had been called cold and heartless, and now she finally knew that wasn't true.

Cold heartless people wouldn't have such amazing and supportive friends as she did. She knew she would never be able to repay them, so she vowed that she would do her best to reciprocate all, if not more, the things they did for her. She would be the best friend to them she could possibly be and let them know how much she loved and appreciated them. She wouldn't hold back anymore.

"Thank you,Wendell. I really appreciate that."

Six months later, Brennan sat in her hospital bed, with Angela, Wendell, and Jack beside her. Jack and Angela were holding her newborn twin boys, while Wendell sat in a chair beside Brennan's bed. The nurse walked in and smiled at the people gathered around her patient's bed.

"Ok, mom. I need the names of you babies so that we can make it official." Brennan watched her friends and babies as she told the names. She looked at Jack first,

"The oldest will be Liam Angelo Brennan and Cori Jackson Brennan." Hodgins and Angela smiled at her. "Ok. You guys can go home tomorrow, make sure you have everything you need."

"Thank you all for being here. You all helped me to get through this and I love you all very much," They all leaned down and hugged her.

"Ok, so Jack and I have a gift for you, which you will see tomorrow. Wendell is staying with you to help at night, but we will all be helping with these little monkeys. Rebecca will be bringing Parks by in the morning before we leave in the morning and he will be spending a whole week with you guys.

Brennan was excited. She hadn't seen Parker for a few weeks because he had went to stay with his grandparents in San Diego.


	3. Chapter 3

Excuse My mistakes. Didn't have time to proof read. BTW: a special someone appears in the chapter. As promised its twice as long as the others. Sorry it's a bit rushed i'm in school and I only had thirty minutes to write the chapter. but enjoy!

Disclaimer: I don't own bones, and this is the last time i post this.

* * *

Brennan and Angela discussed transportation for tomorrow, but soon visiting hours were over. They all left Brennan to sleep and prepare for the day to come. Angela and Hodgins came as soon as the visiting hours started and brought the baby bags, clothes for mom and babies, and the carriers. It was times like this that Brennan was happy to have friends like them. Wendell arrived soon after and was accompanied by Rebecca and Parker.

"Hi, Temperance, how do you feel?" Rebecca saw the babies, already in their carriers and smiled.

"Sore but good. Hey, Parks, would you like to meet your little brothers?" Parker looked up at Brennan with the 'can I really?' look. Brennan nodded and showed him over to the twins. She saw Rebecca, from the corner of her eye, back away and wave at her before turning and leaving the room

"This is Liam," Brennan said kneeling in front of the baby carriers, "and that is Cori." Parker looked and awed at his siblings.

"How can we tell them apart?" Parker was being sincere and was very confused because they looked exactly alike.

"Well, Liam likes the color green and Cori likes blue. Usually they will be wearing different colors until we will be able to tell the difference more easily. Now, it's time to go home. You ready?"

Parker nodded, got his stuff and stood by the door with Wendell. She signed the discharge papers and they were on their way quickly. Brennan and the kids rode with Wendell.

"Wendell, I thought we were going home." Wendell looked back at her.

"We are," he said as he pulled up to a massive mansion. She also noticed that Jack and Angela's house was right next door and was connected by a long glass hallway. Even then that wasn't the only way to get in from the other house. The fence that had separated the yards before was now gone and the land was like one large estate.

"Well, let's go inside and get settled." Wendell got out and grabbed both carriers and Brennan grabbed Parkers hand. The first room she went in was the nursery. She couldn't believe how amazing it turned out. Half was colored black and blue the other black and green with matching cribs. Over the tops of the cribs were the baby's names. On the wall by the closet was a mural of a teddy bear that said "I love you Liam and Cori!"

Brennan put the babies down on their respective sides and laid them down to sleep. She picked up a baby monitor and left the room to explore. As she went through the house she noticed that all the actual colors complemented the black Angela used throughout the house and she loved it.

She discovered that the estate had a basketball court, a tennis court, a game room, several pools, and that Jack had out in Cadillac golf carts for getting around as well as a zip line for his childish side.

"Thank you, Angie. I love you guys." She hugged her friend, who had come over to give her the pass code to the outer gate. They had bought her all new things for the house and she was forever grateful. They had even bought her a few new cars. A Nissan Pathfinder, a Porsche Cayenne and a BMW M4 convertible.

"I don't know if I will ever be able to truly thank you guys for everything that you have done, but I will do my best.

Angela smiled at her friend and told her it was no big deal. They walk out into the backyard to find Wendell, Hodgins, and Parker in the pool. She placed the baby monitor on her hip and sat down on one of the poolside chairs.

Three months later she was sitting on her couch with her best friend and her kids watching TV when the phone rang.

"Hello? Yes? Sure, I would be happy to help her. Ok, Jack, Angela, and I are already in the states so tell her that we will meet her at the lab tomorrow. It is open and she can have all her stuff transferred there. Ok. I'll talk to you later then. Bye." Brennan closed her phone and explained the situation to Angela, who was giving her a confused look.

"That was Caroline Julian. Apparently, Cam had a case that is getting a lot of publicity and she has not been able to solve it, so she is calling in the big dogs." Angela nodded and they sat back and watched TV.

The next morning they headed to the lab early, because they had the kids with them. Both boys had Brennan's eyes and auburn hair, but Liam's hair had grown faster than Cori's. Brennan and Angela sat in Angela's office, while feeding the babies.

Cam walked into the lab, just as Brennan and Angela were coming out of Bren's office from putting the boys down to sleep. The baby monitor clipped to Brennan's waistband looked more like a walkie talkie, so it looked odd but Cam thought nothing of it.

"Dr. Brennan, Angela. How are you guys?" Brennan was about to answer when a sudden wailing came from the monitor on her hip. Both Angela and Brennan booked it for her office and went to get the babies. Cam followed and was shocked to see the babies. "Who are these little ones?" Jack came out to see how the girls were doing and was surprised to see them holding the babies.

He pulled Liam out of Angie's arms and kissed his forehead. "That is Liam and that other little cutie is Cori. And before you ask they are not ours, though I wish they were."

Cam looked confused for a second. Then she got a good look at the kids. She noticed the blue eyes and auburn hair. "They're Brennan's?" She looked to her colleague, who nodded and smiled at her.

"Yeah, I was pregnant when I left for Maluku. I didn't know it at the time though. As soon as I found out I went to Paris and stayed with Angela and Jack. After about three months there we came back. The only people that know outside of us four are Wendell, Parker and Rebecca. That reminds me I have to go get Parks in a few minutes. Ange can you ask Jack or Wendell to help me?"

Angela walked over to Wendell and he came over to help her. As they went into her office she heard a voice she had not heard in a year. "Booth…"

She peaked out the door and saw him talking to Cam and Angela, who were trying to distract him so she could leave. She also noticed a blonde standing next to him, her hand in his larger one. She hurried out the door Wendell in front of her with the carriers.

"Hey Bones!" Wendell heard and turned around to look at Brennan real quickly. She motioned him to go ahead so that Booth wouldn't see the kids. She handed him the keys and turned around to him.

"Hi, Booth. I can't really talk right now, I have to go. I'll talk to you tomorrow, though." She knew it was rude but she didn't want to leave Wendell out for long. She turned and walked out the lab without looking back. She hurried to the car and took her keys from Wendell, accepting a hug from him.

"Don't worry. We are all here for you."

She smiled, kissed his cheek, then got in the car and headed to Rebecca's to pick up Parker. When she had gotten back to the states, Brennan had called Parker to let him know that she was coming back and that he was going to have two new brothers. She loved him and he loved her back. He spent every other day with him and he had even taken to calling her mom. She also grew close to Rebecca who, like Angela, was one of her best friends and did everything she could to help her out.

She was excited to see Parker but she also needed to talk with him. She parked in Rebecca's driveway and got the carriers from the back.

Rebecca opened the door and took one of the carriers from her friend. They walked into living room and sat on the couch, the babies in front of them. Rebecca played with Cori and Brennan held a sleeping Liam while they talked.

"So I guess you heard Booth was back," Rebecca nodded, "Well I can't tell him now."

Becca looked disappointed. "And why not Bren? You said you would tell him when the year was over because you didn't want him thinking about that while in a warzone."

"Bec, I don't want me or the kids to be an obligation that he feels he has to take responsibility for. You might say he wouldn't feel that way but he would. He wouldn't want to be a part time dad again. Also he has a girlfriend now and he seems happy. I don't want to mess that up by dragging him into my life. So can you please not tell him about them? I'm going to have this talk with Parker when we leave so I just need to know now." Rebecca smiled and nodded at her friend.

"Thank you so much for understanding, Rebecca. Well we have to go, Angela and Jack are waiting for us to go to lunch so I'll see you later.

Brennan placed Liam back in his car seat be for walking over to the stairs and calling Parker down.

Rebecca walked them out to Brennan's car and set Cori in the back before walking to the passenger door. She reached in and ruffled Parker's hair.

"Be good, baby. I love you."

"I love you too, Mom." Rebecca then turned to Brennan.

"I love you too, ya know," Brennan stated teasingly.

"Aww, do you really mean it." Brennan had caught on to the sarcasm and teasing fairly quickly and this was their normal good bye. They all burst out laughing. Brennan shook her head and looked to Rebecca.

"I'm really glad that you are my best friend and a part of my family." She said before she started the car. Becca back away and Brennan pulled out of the drive, looking in the rearview to see Rebecca waving at her.

"So, Mom, what are we doing today?" Brennan smiled at Parker.

"Right now we are going to get lunch. We are going to Woodmont Grill today. You'll love it. Back when I used to eat meat they had the best steaks. You'll like it there."

Brennan parked the car at Woodmont and got the twins out of the car, putting them in their strollers. Parker pushed one as she pushed the other through the door.  
She saw Angela and Jack sitting in a booth near the back and walked over to them.  
"Hey Little G-man. What's up?"  
"Hi, bug-man. When we get back to the lab can we play in the ookey room?" Hodgins and Parker discussed what they would be doing when the got back to the lab. Angela picked up Liam and Brennan handed her a bottle to feed him. She grabbed another for herself and picked up Cori.  
"So what did Booth say after I left?"  
"I didn't really stick around. I left after he introduced us to his girlfriend. I told them I had some work to get done, and I left. Though he did think something about you and Wendell being together, to which neither Cam or myself replied."  
Brennan looked at her,  
"So he thinks that I am dating Wendell? When I am not?" Angela nodded. Brennan didn't like it but she wasn't going to argue because she knew Angela would eventually convince her to do it.  
"Fine, but don't tell him I moved. I still have the apartment, so he won't know." They ordered their dinner and talked about their day at the lab. They were soon in their cars on the way back to the lab.  
"Mom, that was amazing. Thanks. Can we go there again sometime," Parks asked hopefully.  
"Glad you liked it, and we can go back sometime soon, I promise. Now, when we get to the lab, your dad might be there. I need you to do me a favor. When he's around you can't talk about Liam and Cori and you can't call me mom, but you can call me Amai, if you want. It means the same thing in Shona. Can you do that for me?" Parker nodded. She parked the car and he jumped out, running straight into the building.  
Brennan smiled at him and watched him run in. She knew that a security guard would let him in, so she took her time getting the boys set to go in. Hodgins came out and helped her carry the boys in. He set them down in her office and took Parker to go play with some bugs. Brennan picked up the kids and walked into Angela's office since the playpens were already in there.  
"Hi, Angie." She said as she set the kids down. "So before I get to work, what do you have?" The victim is not the missing boy. He is Asian and Logan is not."  
"Ok, I'm going to get started on my pre-exam. Can you watch the boys?" Angela nodded and Brennan left.  
She walked into her office and saw Booth sitting there with the same blonde she saw with him that morning. She didn't want to meet her but she knew she would have to soon so she made presence known.  
"Hello, Booth. How are you?" Both looked up at her.  
"Hi, Bones. This is Hannah, we met in Afghanistan. Hannah, this is my partner, Bones."  
"Hi, Temperance Brennan."  
"Hannah Burley. It's a pleasure to finally meet you Temperance, I've heard so much about you."  
"You as well, though I haven't heard from Booth in over a year. So I've never heard about you."  
"Yeah, so how was your Maluku dig?"  
" Great until I left. I went to Paris for a little while. Why'd you leave?"  
"Personal reasons."  
Parker ran in and jumped into Brennan's arms.  
"Jack gave me a snake, can I keep it please?"  
"Yeah. We'll put it in one of the aquariums when we get home."  
She put Parker down and turned him to face Booth.  
"Dad!"  
"Hey bud. What are you doing here?"  
"I came to spend the day with Bones, Angela and Hodgins."  
"Oh, well this is is Hannah. Hannah this is my son Parker. Hannah is my girlfriend." Brennan saw Hannah frown for a second before smiling at Parker.

"Hi, Parker. It's nice to meet you."

"You, too," Parker said, but Brennan could tell he didn't really mean it. She had been around him long enough to know when he was lying or hiding something.

"Parker? Why don't you go hang out in Angela's office. Then we'll go home." Parker nodded and headed into Angela's office, but not before hugging Brennan.

"What do you mean go home?"

"He's coming with me, to my place."

"How did you get Rebecca to let you keep him during the week? She doesn't even let me and you don't know her." Brennan shook her head.

"Actually Booth, I have gotten to know Rebecca quite well over the past nine months. I consider her one of my best friends. She helped me a lot when I came back to the states, as did Wendell, Hodgins, and Angela."

Booth looked shocked and then he got an idea. "Hey, Bones? Can I keep Parker for the night? So he can get to know Hannah better and because I haven't seen him in a whole year."

He figured that if he couldn't get to see Parker on the weekdays then he could through Brennan, but she shot that idea down quickly,

"I'm sorry but no. I get to see Parker but when I have him is the only real time I have with him. I don't want to give that up and anyways today is Thursday. Becca said that he will make sure you get to keep him all next week since you have been gone for a year so don't worry. I have to go now, but it was nice meeting you Hannah. I expect I'll be seeing you again in the near future."

Brennan turned around and left her office, smirking, with a stunned Booth standing behind her.


End file.
